I am running PCA for controlling populations structure in GWAS. I am providing files pedind, pedsnp and bed. smartpca shows this message which I don't quite follow: "number of populations too large. Increase maxpops if you wish fatalx: (makeeglist) You really want to analyse more than 100 populations? Aborted"
I don't have that many populations...I was able to run smartpca before with the same setup. I just added a couple of other samples to my dataset, and now it doesn't work anymore. Any suggestions?
Thanks in advance!